Project Summary Cyclin-dependent kinases (CDKs) regulate cell division and transcription. To understand the mechanisms of this regulation, or to target the CDK network in cancer cells, we need to identify the functions and substrates of specific CDKs. To achieve this goal, we pioneered a chemical-genetic approach combining the specificity of genetics with the speed and reversibility of chemical inhibition, by replacement of wild-type with analog- sensitive (AS) mutant CDKs in living cells. In the next five years, we will combine chemical genetics with functional genomics in novel ways, to establish new paradigms of cell-cycle and transcriptional control, and to discover new pathways that interact with the CDK network, which might be targeted in cancer. The CAK-CDK network in cell-cycle control: Our studies revealed distinct activation pathways for CDKs that act in different phases of the cell cycle; a goal for the next five years is to understand how those pathways are regulated by upstream signaling and linked to cell cycle-regulated transcription. We will investigate how a cascade comprising the CDK-activating kinase (CAK) Cdk7 and its target Cdk4 is switched on in G1 when quiescent cells re-enter the division cycle, and how Cdk7 is specifically down-regulated as cells exit the cycle. CDK regulation of the transcription cycle: Inhibiting transcriptional CDKs perturbs RNA polymerase (Pol) II dynamics in ways reminiscent of cell-cycle arrests and checkpoint failures, but the precise mechanisms still need to be defined. Cdk7 is required to establish a promoter-proximal pause in the transition from initiation to elongation, and to promote pause release by activating positive transcription elongation factor b (P-TEFb, a Cdk9/cyclin T1 complex). We showed that normal Pol II elongation rates depend on Cdk9 activity in fission yeast, and defined sets of human and yeast Cdk9 substrates, which are enriched for proteins implicated in RNA processing. Over the next five years, we will test the idea that Cdk9 acts on different substrates to stimulate both transcription elongation and RNA processing, to ensure their kinetic coupling. Defining a transcription exit network: CDK regulation persists to the end of the transcription cycle; we validated the termination enzyme Xrn2 and protein phosphatase 1 (PP1, implicated in cleavage and polyadenylation) as bona fide Cdk9 substrates. Phosphorylation by Cdk9 activates Xrn2 but inhibits PP1, which is required to dephosphorylate the elongation factor (and Cdk9 target) Spt5. In the next five years we will test the emergent model of a bistable Cdk9-PP1 switch that controls the elongation-termination transition. Chemical-genetic discovery of synthetic-lethal interactions CDKs have emerged as targets of drugs that exploit transcriptional dependencies unique to certain cancer cells. We induced such a dependency in colon cancer cells by combining activators of the tumor suppressor p53 with inhibitors of Cdk7 to achieve synthetic lethality. In the next five years, we will uncover novel pathways that interact with the CDK network?and might lead to anti-cancer drug combinations?by synthetic-lethal screens in human cells dependent on AS CDKs.